Class Hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 123456]

CRDKit::MolOps::AdjustQueryParameters
CRDKit::AromaticAtomIterator_< Atom_, Mol_ >	Iterate over aromatic atoms, this is bidirectional
►CRDKit::Atom	The class for representing atoms
CRDKit::QueryAtom	Class for storing atomic queries
CRDKit::Canon::AtomCompareFunctor
CRDKit::atomicData
CForceFields::UFF::AtomicParams	Class to store atomic parameters for the Universal Force Field
CRDKit::AtomIterator_< Atom_, Mol_ >	A general random access iterator
►CRDKit::AtomMonomerInfo	The abstract base class for atom-level monomer info
CRDKit::AtomPDBResidueInfo	Captures atom-level information about peptide residues
CRDKit::SLNParse::AttribType
►Cbasic_streambuf
Cboost_adaptbx::python::streambuf	A stream buffer getting data from and putting data into a Python file object
►Cbinary_function
CRankers::argless< T >
CRankers::pairGreater< T1, T2 >	Functor for implementing > on two std::pairs. The first entries are
CRankers::pairLess< T1, T2 >	Function for implementing < on two std::pairs. The first entries are
CRDInfoTheory::BitCorrMatGenerator
►CBitVect	Abstract base class for storing BitVectors
CExplicitBitVect	Class for bit vectors that are densely occupied
CSparseBitVect	Class for bit vectors that are sparsely occupied
►CRDKit::Bond	Class for representing a bond
CRDKit::QueryBond	Class for storing Bond queries
CRDKit::Canon::bondholder
CRDKit::BondIterator_	Iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess
CRDKit::Canon::canon_atom
►CRDCatalog::Catalog< entryType, paramType >	Abstract base class for a catalog object
CRDCatalog::HierarchCatalog< entryType, paramType, orderType >	A Catalog with a hierarchical structure
CRDKit::FilterCatalog
►CRDCatalog::Catalog< entryType, orderType >
CRDCatalog::LinearCatalog< entryType, orderType >	Linear Catalog (analogous to an std::vector)
►CRDCatalog::CatalogEntry	Abstract base class to be used to represent an entry in a Catalog
CRDKit::FilterCatalogEntry
CRDKit::FragCatalogEntry
CRDKit::MolCatalogEntry	This class is used to store ROMol objects in a MolCatalog
►CRDCatalog::CatalogParams	Abstract base class for the container used to create a catalog
CRDKit::FilterCatalogParams
CRDKit::FragCatParams	Container for user parameters used to create a fragment catalog
CRDKit::MolCatalogParams	Container for user parameters used to create a mol catalog
CRDKit::charptr_functor	Functor for comparing two strings
►CChemicalFeatures::ChemicalFeature	Abstract base class for chemical feature
CChemicalFeatures::FreeChemicalFeature	Class for chemical features that do not orignate from molecules
CRDKit::MolChemicalFeature
CRDKit::ChemicalReaction	This is a class for storing and applying general chemical reactions
CRDKit::Canon::ChiralAtomCompareFunctor
CDistGeom::ChiralSet	Class used to store a quartet of points and chiral volume bounds on them
CRDKit::FMCS::Composition2N
CRDKit::Conformer	The class for representing 2D or 3D conformation of a molecule
CRDKit::ConstBondIterator_	Const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess
CRDKit::Descriptors::CrippenParamCollection	Singleton class for retrieving Crippen parameters
CRDKit::Descriptors::CrippenParams	Class used to store Crippen parameters
CRDKit::Dict	The Dict class can be used to store objects of arbitrary type keyed by strings
CRDKit::DiscreteDistMat
CRDKit::DiscreteValueVect	Class for efficiently storing vectors of discrete values
►CRDPickers::DistPicker	Abstract base class to do perform item picking (typically molecules) using a distance matrix
CRDPickers::HierarchicalClusterPicker	Diversity picker based on hierarchical clustering
CRDPickers::MaxMinPicker	Implements the MaxMin algorithm for picking a subset of item from a pool
CRDKit::FMCS::DuplicatedSeedCache
CRDDepict::EmbeddedAtom	Class that contains the data for an atoms that has alredy been embedded
CRDDepict::EmbeddedFrag	Class containing a fragment of a molecule that has already been embedded
►Cenable_shared_from_this
►CRDKit::FilterMatcherBase
CRDKit::ExclusionList
CRDKit::FilterMatchOps::And
CRDKit::FilterMatchOps::Not
CRDKit::FilterMatchOps::Or
CRDKit::SmartsMatcher
►Cstd::exception	STL class
CDatastructsException
CRDGeom::GridException
CRDKit::ChemicalReactionException	Used to indicate an error in the chemical reaction engine
CRDKit::ChemicalReactionParserException	Used to indicate an error in parsing reaction data
CRDKit::ConformerException	Used to indicate errors from incorrect confomer access
CRDKit::FeatureFileParseException	Class used to indicate errors in parsing feature definition files
CRDKit::MolAlign::MolAlignException
CRDKit::MolPicklerException	Used to indicate exceptions whilst pickling (serializing) molecules
CRDKit::MolSanitizeException	Class for flagging sanitization errors
CRDKit::ReactionPicklerException	Used to indicate exceptions whilst pickling (serializing) reactions
CRDKit::SLNParseException
CRDKit::SmilesParseException
►Cstd::runtime_error	STL class
CIndexErrorException	Class to allow us to throw an IndexError from C++ and have it make it back to Python
CInvar::Invariant
CKeyErrorException	Class to allow us to throw a KeyError from C++ and have it make it back to Python
CRDKit::BadFileException	Used by various file parsing classes to indicate a bad file
CRDKit::FileParseException	Used by various file parsing classes to indicate a parse error
CValueErrorException	Class to allow us to throw a ValueError from C++ and have it make it back to Python
CRDKit::FMCS::ExecStatistics
CRDFeatures::ExplicitFeature< FAMILYMARKER, TYPEMARKER, LOCTYPE >
CRDKit::FilterData_t
CRDKit::FilterMatch	Holds the atomPairs matched by the underlying matcher
CRDKit::FilterProperty_t
CForceFields::ForceField	A class to store forcefields and handle minimization
►CForceFields::ForceFieldContrib	Abstract base class for contributions to ForceFields
CDistGeom::ChiralViolationContrib
CDistGeom::DistViolationContrib
CDistGeom::FourthDimContrib
CForceFields::CrystalFF::TorsionAngleContribM6	Torsion term for multiplicity m = 1 - 6
CForceFields::MMFF::AngleBendContrib	The angle-bend term for MMFF
CForceFields::MMFF::AngleConstraintContrib	An angle range constraint modelled after a AngleBendContrib
CForceFields::MMFF::BondStretchContrib	The bond-stretch term for MMFF
CForceFields::MMFF::DistanceConstraintContrib	A distance range constraint modelled after a BondStretchContrib
CForceFields::MMFF::EleContrib	Electrostatic term for MMFF
CForceFields::MMFF::OopBendContrib	Out-of-plane term for MMFF
CForceFields::MMFF::PositionConstraintContrib	A position constraint of the type 0.5k * deltaX^2
CForceFields::MMFF::StretchBendContrib	The angle-bend term for MMFF
CForceFields::MMFF::TorsionAngleContrib	Torsion term for MMFF
CForceFields::MMFF::TorsionConstraintContrib	A dihedral angle range constraint modelled after a TorsionContrib
CForceFields::MMFF::VdWContrib	Van der Waals term for MMFF
CForceFields::UFF::AngleBendContrib	The angle-bend term for the Universal Force Field
CForceFields::UFF::AngleConstraintContrib	An angle range constraint modelled after a AngleBendContrib
CForceFields::UFF::BondStretchContrib	The bond-stretch term for the Universal Force Field
CForceFields::UFF::DistanceConstraintContrib	A distance range constraint modelled after a BondStretchContrib
CForceFields::UFF::InversionContrib	The inversion term for the Universal Force Field
CForceFields::UFF::PositionConstraintContrib	A position constraint of the type 0.5k * deltaX^2
CForceFields::UFF::TorsionAngleContrib	Torsion term for the Universal Force Field
CForceFields::UFF::TorsionConstraintContrib	A dihedral angle range constraint modelled after a TorsionContrib
CForceFields::UFF::vdWContrib	Van der Waals term for the Universal Force Field
CRDKit::FPBReader	Class for reading and searching FPB files
CRDKit::FragCatGenerator
CRDKit::FragFPGenerator
CRDKit::MolFragmenter::FragmenterBondType
CRDKit::GasteigerParams
►CGraph_t
CRDKit::FMCS::Graph
►CRDGeom::Grid3D	Virtual base class for a grid object
CRDGeom::UniformGrid3D
CRDDepict::gtIIPair
CRDKit::FMCS::SubstructureCache::HashKey
CRDKit::MolHash::HashSet
CRDKit::HeteroatomIterator_< Atom_, Mol_ >	Iterate over heteroatoms, this is bidirectional
CRDFeatures::ImplicitFeature< FAMILYMARKER, TYPEMARKER, LOCTYPE >
CRDInfoTheory::InfoBitRanker
CQueries::Int2Type< v >	Class to allow integer values to pick templates
►Cstd::ios_base	STL class
►Cstd::basic_ios< Char >	STL class
►Cstd::basic_istream< Char >	STL class
►Cstd::istream	STL class
Cboost_adaptbx::python::streambuf::istream
►Cstd::basic_ostream< Char >	STL class
►Cstd::ostream	STL class
►Cboost_adaptbx::python::streambuf::ostream
Cboost_adaptbx::python::ostream
CRDKit::FMCS::SubstructureCache::KeyNumericMetrics
CRDKit::MolAlign::LAP
CRDKit::larger_of< T >	Functor for returning the larger of two values
CRDKit::Utils::LocaleSwitcher
CRDKit::ltDouble	Functor to compare two doubles with a tolerance
CRDKit::MatchingAtomIterator_< Atom_, Mol_ >	Iterate over atoms matching a query function. This is bidirectional
►CRDNumeric::Matrix< TYPE >	A matrix class for general, non-square matrices
CRDNumeric::SquareMatrix< TYPE >
►CRDNumeric::Matrix< double >
►CRDNumeric::SquareMatrix< double >
CDistGeom::BoundsMatrix	Class to store the distance bound
CRDGeom::Transform2D
CRDGeom::Transform3D
CRDKit::FMCS::MaximumCommonSubgraph
CRDKit::MCSAtomCompareParameters
CRDKit::MCSBondCompareParameters
CRDKit::MCSParameters
CRDKit::MCSProgressData
CRDKit::MCSResult
CRDDataManip::MetricMatrixCalc< vectType, entryType >	A generic metric matrix calculator (e.g similarity matrix or distance matrix)
CForceFields::MMFF::MMFFAngle	Class to store MMFF parameters for angle bending
CForceFields::MMFF::MMFFAngleCollection
CForceFields::MMFF::MMFFAromCollection
CRDKit::MMFF::MMFFAtomProperties
CForceFields::MMFF::MMFFBndkCollection
CForceFields::MMFF::MMFFBond	Class to store MMFF parameters for bond stretching
CForceFields::MMFF::MMFFBondCollection
CForceFields::MMFF::MMFFChg
CForceFields::MMFF::MMFFChgCollection
CForceFields::MMFF::MMFFCovRadPauEle
CForceFields::MMFF::MMFFCovRadPauEleCollection
CForceFields::MMFF::MMFFDef	Class to store MMFF atom type equivalence levels
CForceFields::MMFF::MMFFDefCollection
CForceFields::MMFF::MMFFDfsbCollection
CForceFields::MMFF::MMFFHerschbachLaurie
CForceFields::MMFF::MMFFHerschbachLaurieCollection
CRDKit::MMFF::MMFFMolProperties
CForceFields::MMFF::MMFFOop	Class to store MMFF parameters for out-of-plane bending
CForceFields::MMFF::MMFFOopCollection
CForceFields::MMFF::MMFFPBCI	Class to store MMFF Partial Bond Charge Increments
CForceFields::MMFF::MMFFPBCICollection
CForceFields::MMFF::MMFFProp	Class to store MMFF Properties
CForceFields::MMFF::MMFFPropCollection
CForceFields::MMFF::MMFFStbn	Class to store MMFF parameters for stretch-bending
CForceFields::MMFF::MMFFStbnCollection
CForceFields::MMFF::MMFFTor	Class to store MMFF parameters for torsions
CForceFields::MMFF::MMFFTorCollection
CForceFields::MMFF::MMFFVdW	Class to store MMFF parameters for non-bonded Van der Waals
CForceFields::MMFF::MMFFVdWCollection
CForceFields::MMFF::MMFFVdWRijstarEps
CRDKit::MolChemicalFeatureDef
CRDKit::MolChemicalFeatureFactory	The class for finding chemical features in molecules
►CRDKit::MolDraw2D
CRDKit::MolDraw2DCairo
CRDKit::MolDraw2DQt
CRDKit::MolDraw2DSVG
CRDKit::MolDraw2Dwx
CRDKit::MolDrawOptions
CRDKit::FMCS::MolFragment
CRDKit::MolAlign::MolHistogram
CRDKit::MolPickler	Handles pickling (serializing) molecules
CRDKit::Canon::MolStackElem	These are the actual elements in the molecular stack
CRDKit::Canon::MolStackUnion	Used to store components in the molecular stack
►CRDKit::MolSupplier
►CRDKit::ForwardSDMolSupplier
CRDKit::SDMolSupplier
CRDKit::PDBMolSupplier	Lazy file parser for PDB files
CRDKit::SmilesMolSupplier	Lazy file parser for Smiles tables
CRDKit::TDTMolSupplier	Lazy file parser for TDT files
►CRDKit::MolWriter
CRDKit::PDBWriter
CRDKit::SDWriter
CRDKit::SmilesWriter
CRDKit::TDTWriter
CRDKit::FMCS::NewBond
CRDKit::MolAlign::O3A
CRDKit::MolAlign::O3AConstraint
CRDKit::MolAlign::O3AConstraintVect
CRDKit::MolAlign::O3AFuncData
CForceFields::UFF::ParamCollection	Singleton class for retrieving UFF AtomParams
CRDKit::PeriodicTable	Singleton class for retrieving information about atoms
►CRDGeom::Point
CRDGeom::Point2D
CRDGeom::Point3D
CRDGeom::PointND
CPySequenceHolder< T >	Class to hold sequences (lists, tuples, arrays, etc.) passed from Python -> C++
►CQueries::Query< MatchFuncArgType, DataFuncArgType, needsConversion >	Base class for all queries
CQueries::AndQuery< MatchFuncArgType, DataFuncArgType, needsConversion >	Query implementing AND: requires all children to be true
►CQueries::EqualityQuery< MatchFuncArgType, DataFuncArgType, needsConversion >	Query implementing ==: arguments must match a particular value (within an optional tolerance)
CQueries::GreaterEqualQuery< MatchFuncArgType, DataFuncArgType, needsConversion >	Query implementing >= using a particular value (and an optional tolerance)
CQueries::GreaterQuery< MatchFuncArgType, DataFuncArgType, needsConversion >	Query implementing > using a particular value (and an optional tolerance)
CQueries::LessEqualQuery< MatchFuncArgType, DataFuncArgType, needsConversion >	Query implementing <= using a particular value (and an optional tolerance)
CQueries::LessQuery< MatchFuncArgType, DataFuncArgType, needsConversion >	Query implementing < using a particular value (and an optional tolerance)
CQueries::OrQuery< MatchFuncArgType, DataFuncArgType, needsConversion >	Query implementing AND: requires any child to be true
CQueries::RangeQuery< MatchFuncArgType, DataFuncArgType, needsConversion >	Query implementing a range: arguments must fall in a particular range of values
CQueries::SetQuery< MatchFuncArgType, DataFuncArgType, needsConversion >	Query implementing a set: arguments must one of a set of values
CQueries::XOrQuery< MatchFuncArgType, DataFuncArgType, needsConversion >	Query implementing XOR: requires exactly one child to be true
►CQueries::Query< int, Atom const *, needsConversion >
►CQueries::SetQuery< int, Atom const *, true >
CRDKit::RecursiveStructureQuery	Allows use of recursive structure queries (e.g. recursive SMARTS)
►CQueries::Query< int, ConstAtomPtr, needsConversion >
►CQueries::EqualityQuery< int, ConstAtomPtr, true >
CRDKit::AtomRingQuery
►CQueries::Query< int, TargetPtr, needsConversion >
►CQueries::EqualityQuery< int, TargetPtr, true >
CRDKit::HasPropQuery< TargetPtr >
CRDKit::HasPropWithValueQuery< TargetPtr, T >
CRDKit::HasPropWithValueQuery< TargetPtr, std::string >
CRDKit::QueryAtomIterator_< Atom_, Mol_ >	Iterate over atoms matching a query. This is bidirectional
Cboost::logging::rdLogger
CRDKit::ReactionFingerprintParams
CRDKit::ReactionPickler	Handles pickling (serializing) reactions
CRDKit::ResonanceMolSupplier
CRDKit::RingInfo	A class to store information about a molecule's rings
CRDKit::FMCS::RingMatchTableSet
►CRDKit::ROMol	ROMol is a molecule class that is intended to have a fixed topology
CRDKit::RWMol	RWMol is a molecule class that is intended to be edited
CRDKit::MolAlign::SDM
CRDKit::FMCS::Seed
CRDKit::FMCS::SeedSet
CRDKit::SparseIntVect< IndexType >	Class for efficiently storing sparse vectors of ints
CRDKit::Canon::SpecialChiralityAtomCompareFunctor
CRDKit::Canon::SpecialSymmetryAtomCompareFunctor
►Cboost_adaptbx::python::streambuf_capsule
Cboost_adaptbx::python::ostream
CRDKit::FMCS::SubstructureCache
CRDNumeric::SymmMatrix< TYPE >	A symmetric matrix class
CRDKit::FMCS::Target
CRDKit::FMCS::TargetMatch
CRDKit::FMCS::TArray2D< T >
CRDKit::FMCS::TArray2D< bool >
CRDKit::FMCS::DuplicatedSeedCache::TKey
CForceFields::UFF::UFFAngle	Class to store UFF parameters for angle bending
CForceFields::UFF::UFFBond	Class to store UFF parameters for bond stretching
CForceFields::UFF::UFFInv	Class to store UFF parameters for inversions
CForceFields::UFF::UFFTor	Class to store UFF parameters for torsions
CForceFields::UFF::UFFVdW	Class to store UFF parameters for van der Waals interactions
CRDNumeric::Vector< TYPE >	A class to represent vectors of numbers
CRDCatalog::HierarchCatalog< entryType, paramType, orderType >::vertex_entry_t	Used by the BGL to set up the node properties in our graph